Against the Alternate World
by Yanaley
Summary: "Y-you kill your enemies?".. A sudden vision leads to the four brothers being teleported to an alternate world where they discover that one of them is lost to darkness while the other three brothers try to pick up the pieces of their shattered bond. Rated T for language and violence.
1. Chapter 1

_"Attention citizens of New York City, a group of wanted criminals have been reported to have been seen in the Brooklyn district. If you see them, please contact the authorities with descriptions of their appearance and their numbers."_

The sky was a deep shade of crimson... Why was the sky _red_? And the smell of smoke lingered around the streets and seemed to get stronger with each breath. There were massive cracks in the ground and the number of pot-holes in the roads were too many to count, there was also the warm, yet stuffy temperature in the air... almost as if there was an outdoor heater around...

These thoughts came into the head of a sixteen year old girl named April O'Neil as she slowly walked around a deserted ghost town of a city that kept replaying the same message over and over again on giant speakers placed on the larger buildings; "SERVE THE SHREDDER. THE SHREDDER IS ALWAYS WATCHING."

Wait...that was a woman's voice, that sounded astoundingly similar to an enemy-turned-ally of the red-headed teenager as she stood with her mouth agape, not knowing what to do in this wasteland of a city. "Karai hates the Shredder..." she muttered to herself, squinting her blue eyes at several skyscrapers in the distance. "So why is she talking about serving him?"

A loud thud, sounding like a stone smacking into a brick wall, broke April out of her questioning and she quickly sprinted to a collection of alleyway that were shadowed by the large walls and dumpsters shoved narrowly against each other. "H-Hello?" she called, cautiously moving her hand towards the pocket of her denim shorts where she kept her weapon, a small decorated Japanese tessen. "Is there anybody there?" she tried again, chewing on her bottom lip nervously, bracing herself for an attack...that apparently wasn't coming.

Sighing heavily, she slumped her shoulders and moved to turn her back and exit out of they alley when the sound of a deep voice coughing caused her to whip around quickly and unfold her metal fan-blade to defend herself if need be. "I know there's somebody there! Show yourself!" she demanded, putting on a brave face despite her trembling hands saying otherwise.

"Put the weapon down," a voice hissed as light footsteps pattered slowly towards the red-head. "We mean you no harm."

"We?!" April yelped, backing away from the shadows and into the light of the empty streets. A figure stepped into view, revealing their identity as a giant humanoid turtle wearing a long black trenchcoat and dark shades over his eyes. "Wait, _Leo_?!"

The giant turtle, apparently named 'Leo' kept a stoic expression and simply made a grunting sound before cocking his head to one side. "You sound so much like a friend of ours-"

 _April_

A pair of blue eyes and a single green eye lit up from the darkness and startled April enough to jump backwards in fright as a sudden voice seemed to call her name and echo from an unknown location. "What _is_ this? Leo...!"

 _April!_

* * *

" **APRIL**!" another voice ripped through reality and for several seconds darkness...before a sudden brightness... and the image of a middle-aged man with red-hair and wearing polka-dot pyjamas, kneeling next to her bed.

"D-Dad?"

"Oh thank goodness'," he breathed out in relief before moving away from his daughter's bedside and opting to hover near her desk while she sat herself up. "You were talking in your sleep again...about somebody who's always watching?" he placed a hand on April's shoulder. "Is everything okay?"

"It's fine, Dad," she murmured, placing a hand over her forehead with a small groan. "Just another stupid nightmare, that's all. We all get them."

"Indeed we do," he hummed, "but you'd tell me if anything was wrong, right, April?"

"Of course I would," she groaned, flinging herself back into a laying down position. "It just felt so real..."


	2. Chapter 2

**Afternoon everybody! Just to let you all know; this story take place after the Season 4 Finale so if you haven't watched the last two episodes and don't want them to be ruined, this is a warning :)**

 **LeoBlue2012 - There will be a lot of chapters and I'm really glad you do! Thanks! ^^**

 **Smokescreen-ninja - Thank youu! I'm glad you enjoyed the first chapter!**

* * *

"So Leo was stalking you from a dark alley?" Raph snorted, leaning back into the sofa with a piece of pizza held tightly in his left hand. Jerking his head to the side, he smirked over at his blue-clad brother. "Hear that Fearless Leader?"

"Crystal clear, Raph," the older turtle grunted, fixing his red-clad brother with an expression that screamed; I-am-not-amused. "Anyway," Leo turned back to April. "You think it's something to worry about?"

"Well, throughout the dream I had a really bad feeling in my gut," the red-head explained, pausing to take a bite out of her own pizza slice. "Like, really, _really_ bad."

"Or maybe it was because Leo was actin' like a creep in an alleyway?" Raph asked, chewing on the remainder of his pizza before holding his hands up in mock-defense when Leo turned around to shoot him with another glare. "I'm just saying-"

"Hey dudes! Hey April!" the high pitched, excitable voice of the youngest turtle bounced into view with a wide grin. "What'cha doing?"

"Talking," Leo muttered, reaching for another slice of pizza before Mikey got there first. "April said she saw all of us in a dream, but we were different-" Leo quickly made his voice louder when he noticed Raphael open his big mouth, "-We were hiding in an alleyway, _all_ of us," he added, glaring over at Raph pointedly.

"Huh," Mikey shrugged, his eyes fixed on the box of Antonio's Pizza with a wide smile before his face morphed into a serious one. "Wait, where's Donnie?"

The moody response of "Where do ya' think?" from Raphael was ignored as he hurried across the tv area and made his way towards the large metal doors of his immediate older brother, Donatello's lab. The doors were tightly shut which was an obvious sign of 'Do not disturb me' but Mikey rarely paid attention to his brother's loner-nature.

Leo, Raph and April all winced after Mikey's shrill scream of: "DONNIE!" echoed around the lair before another angry voice piped up just as loud as the freckled turtle.

"WHAT ARE YOU DOING?!"

"Hey! Mikey found a rarely-spotted nerd!" Raph cackled pointing a green finger over at a furious looking turtle wearing a purple bandana who stood in the doorway of his lab looking as if he were about to explode.

"Raph-" April muttered sternly, awaiting the drama that was about to unfold.

"I wouldn't be rarely-spotted if I wasn't busy fixing countless things that _you_ broke, Raphael, not to mention my experiments with mutagen!" Donnie mentally stomped his foot. "Oh and I'm _not_ a nerd!"

"Yeah Raph, lay off bro!"

"Shut your mouth, Mikey!"

"Alright that's enough!" Leo commanded, trying to take control of the situation before Mikey or Donnie said anything that would tick his hot-tempered brother off even more. Leo placed a hand on the red-clad turtle's plastron not just to block him from moving towards their younger brothers but to try and calm him down from his sudden rage.

"Don't yell at me, Fearless Leader!" Raph snarled, shoving Leo's hand away with a growl. "Quit acting so high and mighty; you'll never be _Splinter_!"

Mikey let out a gasp before looking at Donnie with sorrowful eyes, moving to embrace his immediate older brother for comfort while April and Leo fixed their astounded expressions on Raph, who looked as if he'd immediately regretted his choice of words. "Aw shit," Raph muttered, rubbing the back of his head while looking away from everybody. "I didn't mean to...You know I wouldn't-!"

"It's okay, dude," Leo forced himself to smile in order to comfort the hotheaded turtle in front of him. "We're all missing him-"

"I think I'm going to go," April piped up, flashing an apologetic shrug at Leonardo before grabbing her bag and quickly moving past the two elder turtles. "See you guys later, yeah?" she added, waving her hand before quickly walking back across the subway tunnels, brushing a stray tear from her eye as the noises from the lair grew more quieter with distance.

Sighing heavily, Leonardo slumped his shoulders and stared at the ground, his brother's following his silence, not knowing what to say. A high pitched beeping noising coming from the lab stirred Donatello out of his own inner thoughts as he abandoned Mikey's side and grabbed hold of his white Bo staff, the top glowing purple and white. "Uh... guys?"

"What's it doing, Donnie?" Leo quickly got up the steps and stared at the patterns on the high-tech weapon, not really understanding the functions of technology that was about three thousand years advanced compared to Earth tech.

"I-I don't know!" Donnie stammered, shaking the staff slightly. "It's been doing this for a while now, but never this long... Think it could be something to do with the Fugitoid?"

"Could be," Leonardo shrugged, squinting at the dotted lights moving around the weapon. "Hang on, what's it doing-!"

A bright flash of light filled the entire lair as the staff levitated from Donnie's hand and unleashed little static shocks and flashes of yellow and white light.

 _"Leo!"_

 _"Donnie!"_

"What's going... ooonnn?!" Leo yelled, panicking when he felt himself be lifted off the ground. A high pitched sound blasted around the turtles as the light began to flash violently and strong wind seemed to pick up from out of nowhere. " _GUYS_!"


	3. Chapter 3

Treading back through the tunnels, April silently cursed herself for rushing off when she should have stayed and comforted the turtles. Their father was dead, of course there were going to be some arguments and tears... She smacked herself in the forehead several times, berating herself for acting like a terrible friend.

"When I get back to the lair, I'll cook them something special," she told herself, trying to picture the reactions of the four brothers; Leonardo would politely thank her, Raphael would pretend not to be bothered but would grunt a thanks, Donatello would be over the top and Mikey would demand to aid her in the kitchen. Giggling, she quickly headed through the turnstiles, "Hi again, guys, sorry that I -" her voice trailed off as she stared at the deserted lair, the tv was still flashing and Donnie's lab doors were wide open.

"Guys?" April called, dropping her bag next to one of the arcade machines and running into the dojo. "Leo?" Not giving up, she left the dojo and peered into the kitchen, "Mikey? Raph?" last option, she headed into the lab, "Donnie?"

 _Where on earth did they go?_ April thought to herself, worry clouding her thoughts. _I was only gone for about ten minutes... I would've heard them leave the sewers..._

* * *

Leo grunted loudly as he flew through the air and landed face first into the dry ground, the light then sent Raph and Mikey hurtling down towards him and the three lay still groaning as the light died down and vanished.

"Okay..." Raph mumbled, his jaw lodged into the ground. "Anybody want to tell me what the hell that was about?"

"I've got a better question," a gruff voice spoke up from behind them as a shining blade hovered close to Raph's face. Leo and Mikey turned around while Raph cursed at a human decked out in armor and weapons in front of them. The wide-eyed expressions of the other two turtles caused the gruff voice to sigh deeply as he stepped forward, revealing his identity; he was a tall, muscular built adult turtle with freckles who wore an orange bandana that covered the top half of his face and eyes. He had several scars all over his shell, plastron and limbs but his most horrifying feature to the younger turtles was that he was missing most of his left arm.

"Where the hell did you three come from?" the older turtle growled, getting up in Leo's personal space while Mikey whimpered behind him. "I don't recall Shred-Head taking on anymore mutant apprentices lately."

"You _three_?" Leo narrowed his eyes before moving back. "There's four-" he turned to his brothers and felt a lump lodge in his throat, said-forth turtle was nowhere to be found. "Donnie..." he breathed, looking around anxiously. "Where's Donnie?!"

"Michelangelo, sir!" one of the soldiers stepped forward with his gun held in both hands. "They're aware of the enemy! They could be dangerous-"

"Stand down," the older turtle ordered, holding out his right hand. "One of them looks exactly like me when I was a teenager. We'll take the three of them back to our hideout for questioning," he frowned at the three, ignoring the whispers of concern from his soldiers before adding, "and if we don't like what they have to tell us, well," his steely blue eyes locked on the younger turtles. "I guess the kiddy gloves will have to come off then, won't they?"

Leo and Raph glared back at the older turtle before finding themselves shoved to their feet by four soldiers, once one smacked Raph against his shell, he made a move for his sai blade but his arm was caught by Leo who shook his head, a silent order not to resist. Mikey trailed along behind his two brothers quietly, repeatedly looking behind him in hopes of his missing brother to suddenly pop out of a tree and tell them what they had to do to get back home. While thinking this, Mikey didn't realise his brother had stopped and bumped right into Raph's shell, sending the two of them falling once again.

Leo quickly moved to pull both of them to their feet and once Raph had shoved Mikey back in the plastron, the older turtle decided to speak up once again: "You asked about Donnie didn't you?"

The three younger turtles glanced at each other before Raph, of all turtles, stepped forward with folded arms. "Yeah, that's right. Why do you ask?" making no effort whatsoever so show respect to these strangers, even if one of them did look like an older version of his little brother.

"Forget about him," the elder snapped. "It'd be in your best interests to move on and forget he ever existed."


	4. Chapter 4

"Hey, hey, hey!" Leo quickly rushed in front of the older orange-clad turtle with a piercing expression and his arms outstretched. "What on earth is that supposed to mean?" he dropped his arms down and added, spitefully, "Are you even _our_ Mikey?"

"I'm this world's _Michelangelo_ , kid," the elder mutant grunted, using his right hand to shove the smaller turtle aside so he could stride forward toward several half-destroyed buildings and pieces of metal wire fence embedded into the thick, dry dirt. "I don't go by my kid name anymore."

"What the actual hell?" Raph muttered, placing a comforting hand on Leo's shoulder before turning to several armed soldiers behind them, "Do you guys know what his problem is?"

Nobody answered Raph's question and simply clicked their weapons at different times, making it obvious that the younger turtles were supposed to be following Michelangelo into the doorway of a crumbling old warehouse, complete with splinters of dusty glass and a cold breeze whipping against their skin.

"Cosy..." Mikey sang, quietly following behind his two brothers while looking around at their surroundings, trying not to be spooked with how...lifeless everything looked. This wasteland couldn't be the thriving, bright city he loved, something seriously felt off about this entire city and it sent chills up the orange-banded turtle's shell just thinking about it.

Slowly walking alongside the armed men and women, the young turtles watched as Michelangelo disappeared into the darkness of the old warehouse before returning, looking as if the chip on his shoulder had grown by an inch. The loud trudging of thick boots making their way through the cracked-dirt ground and the sound of metal screeching in the distance was enough for the turtles to put their guards up, Raphael even moving to grab his sai blades from his belt but was halted when he felt the painful crack of a rifle smacking into his neck.

Turning to the armed soldier who had assaulted him, Raph saw red and moved to launch himself at the human in pure rage but was stopped when he felt the arms of his two brothers yanking him back and pinning him to the ground with all their strength.

"Bad move," Leo grunted, fighting to keep his immediate younger brother still while he continued to lash out. "Quit it! They're all armed, damn it! If you attack, they'll shoot you!"

"That's right, bro!" Mikey added, wincing slightly as Raph tightly clamped his hand down on his shoulder. "We've lost Donnie and Leo and me don't wanna' lose you too!"

"Let go of me, you pair of-"

"Soldiers; stand down!" came a command from the warehouse which was immediately followed as the armed humans stepped back and withdrew their weapons from aiming at the three young mutants who were frozen in their spots. Leo looked over his shoulder once he felt recognition with the voice and felt his jaw drop when the sight of their close friend and ally, April O'Neil, stood close by with her hands behind her back.

As the woman got closer, the three brothers immediately took in the fact that this April was taller, leaner and looked about twenty or thirty years older than their teenage friend. They also noticed the streaks of grey patterned against her red locks and the vibrant blue eyes now seemed to have a greyish tint and a softer look as she regarded them.

"How is this possible...?" she whispered, a gloved hand coming to her mouth as she tried to suppress the childish beam on her face. "Mikey, I almost forgot how adorable you all looked when we were kids!"

Michelangelo simply responded with a grunt before turning his head away towards some old looking leather tires and several broken car engines.

"How old are you all? Fifteen, sixteen? And on another note, how on earth did you get here?" she blinked, pausing her friendly interrogation to look over the heads of the three turtles and her expression morphed to one of sadness. "It hasn't happened already has it?"

"Hasn't _what_ happened?" Raph muttered, folding his arms and frowning at the middle-aged woman.

"Where is he? Where's Donnie?" she sounded almost...frantic, as if the question struck fear into her as well as curiosity before she looked at Leonardo with a pleading expression. "What happened to you all?"

"Where do we start?" Leo groaned, rubbing his head with his left hand, "To make a long story short? We landed here from a big light and then these humans and a moody old turtle," he jabbed his finger in the direction on Michelangelo and the human soldiers, "dragged us here."

"Also to answer your question about Donnie, we don't know where he is," Raph added, looking annoyed, "the light dragged us all here but he didn't land where we did and we need to find him before more lunatics with guns try to kill us."


	5. Chapter 5

Tapping several letters and numbers across the keyboard of an old-fashioned computer, April let out a sigh between clenched teeth as she, alongside three other people, attempted to hack into the entire security system of New York.

"So...why go through all this?" Leo pressed, not completely sure on why April and her colleagues were furiously attempting to access forbidden files and codes. "Wouldn't it be easier to let us look for him on the streets?"

"If only it were that simple," April breathed out, shoving her keyboard aside and swiveling her chair around to face the young turtles. "If you guys are seen, the armies will come after you. No, it's best to wait here and let us delete any footage they have of you three and then focus on looking for your brother."

"Uh, April?" Mikey nervously stepped forward, rubbing his arm. When the red-head nodded at him to show that she was listening, Mikey added, "You know what you just said about us being seen? What are we going to do if they find Donnie?"

"That's right," Raph frowned, striding forward and ignoring the grunt from Michelangelo in the background. "They'll kill him if they see he's alone! We need to get out there and find him NOW!"

"These kids are driving me crazy, April," Michelangelo groaned from the other side of the room, using his good hand to cover his face. He looked over and saw the three turtles' attention on him and he mentally cursed inside his own head. "I'm just saying," he continued, sniffing and turning his head away, "you three have no idea what's going on in this world so listen to what April's telling you."

"I don't care about what you're all trying to do, pal," Raph seethed. "I want to find our brother and get back to our own world, so back off!"

"Technically, Donnie's my brother too," Michelangelo pointed out before shaking his head and twisting his face. "As much as I'd like to deny it."

"What _exactly_ is your problem anyway?" Leo asked, his turn to get angry at the older version of their little brother. His stern expression dropped when Michelangelo left his spot and soon found himself up in the blue-clad turtle's face and Leo was forced to take a step back. "What have you got against our family?"

"Family," Michelangelo's lip twisted into a cruel smirk. "Don't make me fucking laugh, kid."

Leo, Raph and Mikey froze at the harsh curse that had just come out of the orange-banded turtle's mouth. Before any of them could answer Michelangelo's little remark, April's cheer gained their full attention when they saw she'd managed to get into some of the footage from the city.

"YES!" she beamed, accessing dates and times from the cameras and making quick work of deleting several recordings of their resistance group wandering the streets of the city. "We'll be able to find Donnie's whereabouts and then we can work on sending you boys back," April winked at the teenagers before bringing up several different folders.

"Miss O'Neil," a voice of soldier spoke up and he stepped into view, saluting before continuing. "I think that Master Michelangelo is right about this plan, perhaps we shouldn't look for the purple one," he glanced apologetically at the sorrowful faces of the other three turtles. "I mean no offence to you, I have the utmost respect for each of you three but..."

"But it's a foolish plan to track him and bring him back to our base; our _secret_ base!" another soldier yelled from the background, a woman's voice to be exact. "Surely you must see the risks involved, Miss O'Neil?"

"Now listen here-"

"April?" Mikey whimpered, clutching the woman's arm and looking up at her, his lip trembling. "Why don't they want to help Donnie?"

April froze from lecturing her soldiers and turned to Mikey, biting her bottom lip and trying to think of the right thing to say... _He was always the most sensitive of them..._

"Shall I answer that or do you want to do it?" Michelangelo muttered, standing beside April with a bored look on his face.

"M-Mikey..." April began, looking over at the two other turtles. "Leo and Raph, too... It's been thirty years since we were teenagers ourselves and we all," she glanced at Michelangelo, "changed."

"You can say that again," the elder turtle snorted, placing his hand on her shoulder as a comforting gesture. "What she's trying to say is that we all changed when the Shredder was able to stabilize his mutation and do you know who helped him to do that?" he narrowed his eyes at the three younger mutants who looked as if they knew the answer to his question. "This person also turned against his family and killed a lot of people, innocent civilians and...good friends of ours."

"No way..." getting the hint, Raph clenched his hands into fists. "There's no way in _hell_ Donnie would ever do any of that!"

"No, that's right," Michelangelo gritted his teeth. "Not in your world, _yet_. But you wait, give him a few more years and he's going to turn against you. Let me ask you this, kids," the orange-clad turtle sucked in a heavy breath of air, "how's Splinter doing?"

There was a pained silence as the three teenagers looked on the ground, refusing to answer the question they had been given.

"He's already dead in your world, isn't he?"

"MIKEY!" April scolded, pushing the taller turtle away. "What has gotten into you?!"

"I'm warning them!" Michelangelo roared, shoving April's hands off of him. "They need to know! If Father died, then they've only got a little time left before their own world goes to shit!"

The sound of feet racing out of the door alerted April to the younger Mikey running out of the room as fast as his feet could carry him while the other two brothers stood watching the two adults in pure silence with their eyes widened in complete horror.


	6. Chapter 6

Understandably, Donatello was not having a good day. He and his brothers had been having a normal afternoon in their lair and suddenly found themselves pulled into a void of light and then once he had finished falling, he had landed several miles outside of New York city and had been forced to walk back along the long road to find his family.

"I hope Leo, Raph and Mikey didn't land miles away from the city either..." he muttered dryly to himself, walking through several empty streets and corners, seeing no reason to hide in the shadows if there were no humans around. However, once he heard the sound of several heavy footsteps close, he quickly darted into a gap in one of the walls and scurried up an old rusty ladder that led to the rooftop.

Looking over the edge, he let out a tiny sigh of relief when hulking great robots marched past his previous hiding spot, appearing to be scanning the entire area but for what reason was beyond the turtle's thoughts as he moved away from the edge and turned on his heel to head towards the central part of- Wait. A chill ran down Donnie's shell as he looked at the massive skyscrapers in the distance and he clutched his arms in dread at the various symbols of the Foot Clan which were displayed on billboards, neon signs and even huge symbols on the buildings.

"What the heck..." he muttered, his earlier relief cast aside as he suddenly realised the potential threat and danger he and his brothers were in if his suspicions were correct about this world. Silently, Donnie began to count the several names who were affiliated with the clan who had a vendetta against his family. _We can scratch Karai and possibly Storkman off the list_ , he thought dryly to himself.

A sudden loud screech of metal against the ground startled Donnie enough for him to jump to his feet with his hand on his Bo staff, ready to defend himself if he had to, however he was soon stopped when an explosion erupted from the next street over from where he was standing. Quickly dropping his hand, he leaped over the rooftops and sprinted towards the heavy trail smoke and the red flicker of flames.

Peeking over at the mess on the tarmac, he squinted at several shiny objects embedded in the thick metal and with a sigh at his own curiosity, he jumped down and cautiously made his way over to the blazing metal. Carefully pulling one of the shiny blades from the metal and rubbing it on his hand to clean it from the smoke stains, his heart began to thud hopefully when the recognisable symbol of his family crest was carved on it.

"CITIZEN STATE YOUR IDENTIFICATION CODE!" a robotic voice commanded from behind the purple clad turtle, startling him greatly as he dropped the Hamato shuriken. Blinking at the design of the robot, he stared in utter confusion as it looked like a metal version of Splinter's biological daughter...

"Karai?!" Donnie exclaimed, his hand once again moving to snatch his Bo staff from his harness.

"STATE YOUR IDENTIFICATION CODE OR BE DESTROYED!"

"Crap..." Donnie muttered, watching as the robot pointed a blaster-like hand at him and began charging up to attack. As soon as the bullets let loose, he quickly began to dodge them while attempting to find a way to get away. Glancing at the wooden staff in his hand, he made his decision and sheathed it, quickly turning on his heel and fleeing the scene. Although he mentally ridiculed himself for being a coward, he reminded himself he needed to find his family before leaping into a situation that might possibly get him killed.

Before Donatello could make a move to head in the opposite direction of the crazed robots on their killing spree, a familiar large reptilian form charged at the mechanical drones which fell down like bowling pins. With one loud roar, the creature used their large mouth to snap limbs and heads off of the Karai-bots.

"L-L-" Donnie stammered, watching the creature's destruction nervously. " _Leatherhead_?!"

The mutant paused, breathing heavily before turning to face the smaller reptile with a look of bloodlust in his narrowed eyes. Donnie quickly noted the withered scales on Leatherhead's body along with the heavy panting and many scars scattered across his body. "You..." the alligator snarled, his tail flicking around aggressively. " **DONATELLO**!" he roared, his eyes glossed over as he launched himself at the the terrified turtle.

Donnie gulped and weakly tried to fend off the furious mutant with his Bo staff, using the wooden pole to vault over the giant alligator in an attempt to get to higher ground, only Leatherhead snatched the weapon in his hand and applied enough force to turn it to splinters, causing Donnie to lose his footing and fall down onto the streets below, thudding painfully plastron-first.

Groaning softly at being winded from the fall, Donnie lay still focusing on stilling his breathing despite the fear within him, Leatherhead hadn't acted so hostile to him or his family in ages...so _why_ was he trying to crack his shell open?

With another groan, Donnie forced himself to crawl into the darkness of the alley, half tempted to crawl into his shell when he heard the enraged bellow of the mutant alligator above the building alley he was currently hiding in. "I don't know what to do..." he murmured to himself, shutting his eyes tightly as he leaned his shell against a dumpster.

"You've got some nerve comin' round these parts of the city," a gruff voice from the darkness grunted, starting the purple clad turtle and causing him to fumble around his belt and harness in an attempt to find his shell-shaped cell phone.

"Who...Who's there?" Donnie stuttered, grabbing his t-phone and switching it on, the device lighting up the darkness slightly so he could see his near surroundings. He almost dropped his phone when the large form of his immediate older brother turned around and revealed his face, one emerald eye glowing in the darkness while the other eye-hole had been sewn shut. Donnie let out a gasp and his face paled as he stared at the figure, "R-Raph?"


	7. Chapter 7

Being grabbed and then slammed against a cold and damp wall by a psychotic older version of his hotheaded brother was enough for Donatello to finally hold back his own fear, openly trembling in the hands of the older mutant. The fear intensified when Donnie found the sharp point of one of his brother's sai blades aimed between his eyes.

"Did you come to test out your new robots for your boss, Donnie?" Raph hissed, tightening his hold on the younger mutant. "Didn't really think about our allies while hiding behind your stupid tin-can army, did ya'?"

"I don't know what you're talking about!" Donnie protested, his both hands clutched around the larger wrist pinning him to the wall. "Raph, it's _me_!" his brown eyes met Raph's green eye in a silent plea. "It's Donnie."

"I...uh," Raph's hardened expression dropped and replaced with one of confusion. "I know who you are...But..." his eye darted around as if expecting somebody to pop out from the shadows. "What're you plannin'?"

"Planning?" Donnie blinked, wincing as Raph tightened his grip on his plastron. "I don't understand-" he cut himself off when Raphael released his hold and pulled the sai away from his face.

"I should kill you," Raphael grumbled, his hands covering his face. "I want to kill you _so_ bad for everything you've done to us, hell, you deserve worse than death!"

"Stop saying that!" Donnie exclaimed, looking offended. "I haven't done _anything_ , Raph! I've just been looking for you, Leo and Mikey!"

"Leo and Mikey..." Raph's expression changed once again as he whirled around to face Donatello with a hard glare. "You fuckin' stay away from them!"

"Raph, stop this-"

"I should let Leatherhead rip you to shreds after everything you did to him," Raph growled, grabbing Donnie's wrist and yanking him forward roughly. "But Master Splinter would never have wanted us to kill each other, fortunately for you. Yer' lucky I'm the one who found you and not Leo or Mike."

"Right will you just _quit_ it, already?" Donnie ripped himself away from Raphael furiously. "I haven't done _anything_ to Leatherhead and I certainly haven't done anything to you, Raph! What the heck is your problem?!"

"Hang on..." Raphael squinted his good eye at Donatello before pulling out a chipped and cracked version of the T-phone, the screen illuminating Donnie's face and earning a gasp of shock from the older turtle. "You...You're just a kid!"

"Technically I'm a teenager," Donnie piped up, immediately having to correct his brother. "And uh...yeah?"

"This is fucking weird," Raphael shoved the phone back into the pocket of his leather jacket and placed a hand on his head. "Donatello, let me see your left shoulder!"

"Sure..." Donnie began, slightly puzzled with the constant changes in Raphael's attitude towards him. Doing as the older turtle had demanded, Donnie shifted to his side and Raphael stared hard at his shoulder with a face of concentration before the two turtles met each others gazes.

"You...You don't have the Foot symbol..." Raphael's hardened expression fell and he looked like he was about to burst in tears, his lip even trembled. "I...Donnie, I'm sorry..." he stammered. "It's been thirty years bro..."

Those last words seemed to slow time around for Donatello as he simply stared back at Raphael with a picture of terror on his own face. _Thirty years?!_ "Raph..." Donnie spoke up, trying to hide the nervousness in his voice while dreading the answer. "What's happened to the city?"

 _And why are we thirty years in the future...?_

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 **A/N ~ I do apologise for the shortness of this chapter... I didn't want to drag this one on with filler bickering or anything :S Also apologies for the recent slow updates, I actually moved out of my parents house the other week and I've finally settled down properly haha... Thanks for all the comments, favourites and follows, they mean so much! x**


	8. Chapter 8

**A/N: Good evening! I'm so sorry updates have been a bit slow, I just got back from visiting my parents for the week. I got to watch the first few episodes of Season 5 last week before I caught my train and I can't wait for the turtle tots episode, it looks adorable haha! Faster updates now I'm back home ^^'**

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Glaring over at the two younger versions of Leonardo and Raphael, Michelangelo let out a deep sigh and rubbed the temple of his head with his right hand, "Aren't you going to go after the other one? I mean, he had no idea how dangerous the city is outside this base-"

"Not until you explain yourselves," Leo demanded, looking over at Raph and the two nodding in a silent understanding. "Besides, Mikey wouldn't leave this building, he was probably just sick of you all badmouthing our family. I guess it must sting," Leo's piercing eyes locked on Michelangelo. "Seeing yourself in the future being a non-empathetic ass."

Michelangelo drew in a sharp breath after Leonardo's insult, his hand moving towards the nunchucks tucked away in his belt, itching to beat some sense into the cocky little mutant. However, a calming hand from his red-headed friend was enough for him to pause and glance at her with a questioning look on his face. "They don't understand, Mikey," she said firmly, tightening her grip on his shoulder. "Remember, they're still your brothers, and," she bit her lip in the younger turtles' direction, "you need to understand, they've come from a different world to this one. Take it easy."

"Fine," Michelangelo grunted, jabbing his finger at the two younger turtles. "You want to know? Then fine; our brother, Donatello, is a damn psychopath and works as an ally to Oroku Saki," his expression hardened. "The Shredder; the man who murdered our father _twice_ now is being kept alive by our own flesh and blood. Donnie up and left our home years ago and disappeared for a while before we found him again; standing beside Shredder and his other lackeys when they attacked our lair. He cut out Raphael's _eye_ , for God's sake."

"Mike-"

"And then he watched as Shredder pinned me down and did this," Michelangelo spat, pointing at his left arm, his shoulders dropped and his anger morphed into a wounded one as he shielded his eyes. "He smiled while I was bleeding to death on the floor, Leo... I'm... I'm his younger brother," Michelangelo's eyes softened and the younger turtles were finally given a chance to see that their brother's sensitivity still remained, despite being hidden by defensive anger and bluntless. "He blinded Raph in one of his eyes and then he walked away from me while I was lying in a pool of my own _blood_ , man..."

April stood silently, keeping her hand on her friend's shoulder in a comforting gesture, desperately wanting to speak up and say _something_...But what _could_ she say? Everything the orange banded turtle had poured out was true and those memories had left deep scars on her once fun-loving, hyperactive friend and it broke her heart into pieces.

Both Leo and Raph hadn't said anything either, silently processing the words Michelangelo had just spoken, the red-clad turtle had even brought a hand up towards his eye before looking at his blue-clad brother with fearful eyes. Would their Donnie really do such a thing? Would he deliberately torture them and laugh as they were in agonising pain?

 _Everybody can be pushed to their limit... What if something had happened to make Donnie snap...?_

Before Raphael could surround himself in darker thoughts, the steadying grip of his immediate older brother snapped him out of it with three words, "Let's find Mikey," and the two turtles quietly turned and headed out of the double doors of the control room. April and Michelangelo studied the doors silently as they shut behind the younger turtles before regarding each other with stern expressions.

"They're children, Mike and they aren't even from this world to begin with," April muttered, leaning against one of the desk chairs. "Can't you at least try to use less morbid facts around them?"

"Let me ask you something, April," Michelangelo looked up at April with a cold expression. "Was everything that just come out of my mouth a lie? Or was it the truth?" the silence of the woman seemed to have a silent response to the older mutants demand and he snorted before turning his back on her. " _Exactly_."

* * *

"Mikey?" the leader in blue called frantically, dodging past several armed men and women who shot the two turtles suspicious glances.

"There!" Raph yelled, jabbing his finger in the distance where a small turtle was stood in front of a large wooden cabinet, staring up at the objects in the glass with a sorrowful expression. "Uh? Earth to Mikey...?" Raph called as the two older brothers reached the orange clad turtle, who had finally turned to face them with his eyes brimming over with tears.

"Leo, Raph..." Mikey whispered, looking at both turtles before glancing at the cabinet once again. "Casey and Shini are _dead_..."


	9. Chapter 9

**I just want to thank all of the reviews, favourites and follows this story is receiving, I appreciate this all SO much and it really helps me grow more confident with sharing my stories with everybody (seriously, I was so nervous to create an account for a while)... Stay awesome guys!**

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"You serious?!" Raph shoved Mikey aside and staring at the small slab of rock with CASEY JONES carved into it, a rusty metal mask and a chipped hockey stick lay beside it. "No freaking way..." the hotheaded turtle trembled, his emerald eyes never leaving the stone.

"Raph..." Leo moved to place his hand on the red-clad turtle's shell but Raph pulled away from him as if his hand was on fire. Mikey stood beside the leader in blue, whimpering about Shinigami's death; there were several charms and photographs beside the slate with her name on it. Squinting at one crumpled photo in particular, a lump soon grew in Leo's throat as the image of a middle-aged Karai stared back at him.

"I see you found the memorial stand..." April's voice piped up from the background as she slowly made her way over to the three younger turtles with her arms folded and wearing a sorrowful expression.

"What. Happened," Raph choked out, not even looking at April and instead continued to stare at the cabinet window.

"The Shredder happened," April sighed, fidgeting around on the spot, not knowing where to start; "Casey Jones died a hero," she finally decided, a sad smile appearing on her face as she lost herself in old memories. "That bonehead took on Shredder's robot army alone while he waited for our backup...So there he is," she sighed again, still smiling, "rushing into the fight and smashing everything in sight and then Saki arrived on the battle field and caught him off guard. Casey died with that _stupid_ smile of his whilst flipping the Shredder off."

"Your the _man_ , Jones," Raph breathed out, his hand on the panel before he bowed his head in a silent prayer before turning to April. "Did you guys bury him or...?" he wasn't sure if he wanted to hear the answer, luckily his worry faded when April nodded in confirmation to his question;

"Yes, we buried both him and Shini," April sadly glanced at the cabinet once more, "back at my Farmhouse. We like to keep these here though to honour their memories, you know?"

"I would've loved to have seen him before that happened..." Raph mumbled, glaring at the concerned glances that came from his two brothers. " _WHAT_? He died telling Shredhead to suck it!"

"And Shinigami?" Mikey pressed, deeply wanting to know the fate of the beautiful woman he had fallen for after Renet had returned to her own timeline.

"Undercover mission gone wrong," April explained, quickly whirling around to the double doors anxiously before continuing: "Shini and Mikey teamed up to-" a high pitched noise screeched through the entire base, startling everybody as soldiers began to rush into the control room in a silent panic. April turned to the three brothers, her stare firm and serious, "You three get back into the control room _now_."

"Wha-" Leo stammered as April shoved them aside and quickly rushed to the opening of the warehouse, clicking in a code and hastily pulling down the metal doors. "April, what's going-"

"Didn't I make myself clear?" she bellowed, locking the door handles to the ground and the area grew darker as the light from outside was shut out. "I told you to get back in there!"

"April?"

" **NOW**!"

The largest screen in the control panel was dotted with static as all of the rebellion stared up at it in a fearful silence, the younger turtles stood watching the static, not noticing the grunt or roll of eyes from the older Michelangelo before words appeared: SERVE THE SHREDDER. THE SHREDDER IS ALWAYS WATCHING.

"Leo?" Mikey whispered, clutching his oldest brother nervously. "What's happening?"

"I-I don't know," Leo answered, trying to hide his own worry as the image a de-mutated Oroku Saki walked into screen view and sat himself down, complete with spiky armour, bandages wrapped around the areas of his body that weren't covered by metal armour and his Kuro Kabuto helmet that hid his glare.

"Citizens of New York city," he stated, his tone of voice emotionless. "As you know, my rule is being threatened by those hideous turtles and their pathetic human allies!" he banged a spiked hand on his desk before composing himself and sitting up straighter. "My sensors picked up footage of the rebel Michelangelo breaking into one of my work facilities and breaking out several foolish traitors who went along with him. The ones who remained have been executed to send a message to any fools who think to leak intel to the rebellion."

"Shit," the elder turtle cursed, angrily slamming his shell against the wall. "He killed all those innocent people? They had nothing to do with-"

"Ssh, Mikey," April whispered, kind but firm. "We need to see where tinface is taking this."

"And if any of you rebels are watching this broadcast and I _know_ you are!" Shredder bellowed, his calm act dropping as he jabbed a bandaged finger at the camera filming him. "Your days are numbered! Soon I will find out where your new lair is and then I will kill every last one of you disgusting, pathetic-" the Shredder began to ramble furiously, his arms flailing around like a child throwing a temper tantrum.

"What else is on?" April muttered sarcastically to Michelangelo, earning a snort from the older turtle.

Before anybody in the base could speak up again, the Shredder cursed loudly and clutched his arm which was beginning to throb, a piece of Saki's flesh suddenly ripped out from under the bandages and bright green veins spurted from his arm. "DONATELLO!" he yelled and the three younger turtles all watched, eyes wide with fright as a future version of their brainy brother stepped into view wearing a black bandana and a mark of the Foot clan burned on his shoulder. He brought forward a tray with a vaccine full of blue liquid and quickly injected it into the mutating arm before bowing his head and backing away without a sound.

Whatever went on from there on, the three brothers didn't even bother to listen, they just stood there looking at each other while the room around them began to echo and go in slow motion. Leo turned to the older Michelangelo with a look on his face that seemed to ask _"Why?"_ and the older orange clad turtle frowned before speaking up, his voice loud and clear;

"I told you before didn't I? He's not our brother anymore."


	10. Chapter 10

**Oh my gosh! It's been so long since I updates , I am SO sorry! I moved away from my parents' a few months ago and now have finally settled into my new home, after having to sort out all the usual boring stuff like bills, furniture, water blah blah blah... Updates will be more frequent now! Thanks for all of the reviews, faves and follows, truly appreciate it! :)**

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"Find him now!" Raph screamed angrily in April's direction, completely ignoring the sudden amount of people who stood in his way of getting to the red-headed woman. "Find Donnie and then he can help you send us back home!"

"Raphael, calm down!" Leo scolded, raising his voice despite his immediate younger brother appearing to pay no attention... _Oh jeez_ , Leo thought to himself, watching Raph's body twitch and tremble. Showing not signs of complying with the leader-in-blue's order, Leonardo decided to take another approach and grabbed his brother's shoulders tightly.

Success! Raph's attention was now completely on him, his breathing getting heavier as he popped his knuckles every now and again, making it clear that he wasn't happy with what Leo was attempting to do; meanwhile Mikey stood a couple of steps away from his two older brothers, making a gesture or a small sound every now and again but not daring to get involved.

However, Michelangelo watched from a short distance, slouched in a revolving chair, slightly amused at the younger turtles behaviour with their situation.

"Listen to me," oddly soothing and calm, Leo continued, softening his grip on the red-clad turtle. "This is their world, they know more about what's going on and if there's one person here that we can trust more than anybody? It's April. She will _find_ Donnie and we will _help_ her, in however we can, right?" blue eyes locked on to emerald green ones. "It'll be okay, just put some faith into the people here, Raph, and then we can all go home..." he looked over at the static covered screen which had previously shown the Shredder and an older version of their brother. "Together..."

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Standing speechless as he watched the broadcast from one of the city's large screens, both Donnie and Raphael had ditched standing in the dark and damp alley and had moved to another rooftop. However, when the younger turtle had witnessed his older counterpart standing beside the Shredder, pure shock and fear found it's way into both his mind and heart.

"This can't be right," Donnie swallowed thickly, rubbing his arms for warmth due to a sudden chill in the air; whether it was the temperature of the city or his fright for this universe, he was unsure. He turned to Raphael, regarding the older turtle with a torn expression. "I _can't_ be on the Shredder's side! He's hurt us so much...Wh-Why am I standing beside him?!"

"It's...complicated, Donnie," the older red-clad mutant answered, slumping his shoulders as the video feed cut off and turned to static. "We need to move, alright? Leo and Karai are always patrolling and this whole thing will get ugly if they find us-"

"Wait!" Donnie held up his hands, looking flabbergasted. "Leo and Karai? They're here?" a grin found it's way on Donnie's face as relief began to flood his previous worries about his brothers whereabouts...only it lasted for about a minute before Raphael chose to speak up again;

"Uh yeah... Long story short: our Leo is nothing like the Leo you're probably used to. He would happily kill Donatello if given the chance...So we need to go, like, _now_ , Donnie."

"K-Kill...?"

Raphael stood motionless, staring into the large mahogany eyes of Donnie and his own heart tugging at the memories of his own youth. He placed a roughened hand on Donnie's smaller shoulder and leaned down to the purple-clad turtles' eye level. "We need to move, Donnie. I'm sorry but it's not safe in this part of the city, come on," without another sound, Raphael grabbed Donnie's wrist and the two leaped down from the rooftop and quickly blended into the shadows of the alleyways beneath...


	11. Chapter 11

The sun was beginning to set and paint a dark blanket over New York, Raphael had been leading Donnie in and out of darkened streets and abandoned houses and apartment blocks for hours and both turtles were starting to feel the sharp chill of the evening air. Donnie had been continuously been asking if they were close to the hideout for the last two or so hours and Raphael was beginning to feel more and more exhausted with each step.

"Are you sure this is safe?" Donnie questioned, wavering slightly as he followed Raphael up a long flight of rusted metal steps that was once part of an apartment block that looked down on the once lively city...before many buildings were burned down to locate members of the resistance...

"Stop yer' flapping and just trust me, Donnie boy," Raphael grunted, pausing to take a few deep breaths before attempting to straighten himself, wincing when his legs popped and cracked. When he noticed Donnie's concerned eyes on him, the older mutant let out a heart chuckle and slapped the smaller turtle on the shell. "I'm getting old now, Don. Can't run up them high places like we used to, eh?"

"I...guess not," Donnie answered, his voice small as they finally reached the top and was able to witness Raphael's 'stealthy' movements by shoulder charging an old half-eaten wooden door and sending the red-clad turtle straight into a large room lit with a couple of old candles, the melted wax dripping down the floorboard holes.

"Raphael, my brother," a hardened voice rumbled from the darkness as a few large shapes moved around in the darkness. A massive spiked hand reached forward and clasped onto Raphael's own hands and held on tightly, like a greeting. A pair of dark eyes focused in on Donnie and widened slightly upon recognising the younger turtle; "You weren't kidding when you told us you found a tiny Donatello wanderin' the steets, huh!" he cackled. "How's life been treatin' ya lately, hm? Still part of Michelangelo and O'Neil's team or have you decided to go alone again?"

"Takin' a break from the team," Raphael grunted, seating himself against several crates and leaning back. He bent down and lit another cigarette with the flames from the candle and took a drag, "I ran into Leo the other week, out playing vigilante with Karai."

"Are him and her still banging?" Slash boomed with laughter, Raphael joining in, although a lot more reserved while Donnie squeaked in alarm, shuffling closer to Raphael when he heard the sound of a door opening.

"Vulgar reptiles," a familiar voice quipped in as a mutant monkey suddenly walked into the candlelight, yawning and rubbing his head. "What on earth could be so funny about Leonardo's-" he paused, realising the smaller shape beside Raphael which caused him to groan. "Why have you brought a child with you, Raphael?!"

"Look closer, doc," Slash pointed out, not even bothering to shove the light closer to the other two turtles. "It's a familiar face, yeah?"

"Oh my word!" Rockwell climbed over some old boxes and got closer, a bit too up and personal for Donnie's liking but he remained silent. "Donatello seems to have de-aged! What are you doing here, dear boy?"

"I lost my brothers," Donnie answered, his usual attitude while around Doctor Rockwell was cast aside and replaced with worry and nervousness. "I'm worried about them," Donnie added, desperation in his voice. "Have any of you seen them? They're-"

"Easy, Don, settle down," Raphael rested a heavy hand on Donnie's shell. "These guys will vouch for me on this; I have no doubt that Mike and April were able to find them," his green eye softened with kindness. "When morning comes round, we'll contact April and you'll see."

"I hope so," Donnie murmured in defeat, sighing softly as he leaned against Raphael for warmth. His eyes focused on one of the cracked windows and he shut his eyes tightly in a silent prayer. "Goodnight guys, see you soon."

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"We've got loads of rooms for new members and the injured so just stay in here until we send for somebody to escort you in the morning, right?" was the order April had given the three younger turtles after escorting them to a small bedroom. She hadn't stuck around and instead had briefed them on directions and then left in a hurry. Raph had loudly guessed it was probably to do with Michelangelo having another meltdown but then stood with his armed folded, now in a mood after Leo had lectured him on tact.

"Maybe we should sleep together tonight?" Leo pressed, trying to change the subject while unbuckling his harness and removing his belt and knee pads.

"Yeah, dudes," Mikey agreed, half asleep on the bed while still wearing all his gear which earned collective sighs from his older brothers. After managing to remove Mikey's belt and nunchucks, Leo and Raph joined their younger brother on the bed and snuggled into the white sheets. Huddled together, the turtles allowed sleep to consume them and then tomorrow they'd join April and Michelangelo in finding their missing brother...Tomorrow, they'd be reunited... right?

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 **So yeah, a tiny little section for what's happening with the younger turtles at the base... I don't want to write loads of filler as I want them all to be reunited ASAP ;_; I'm trying to write sainw!Raph the way the 2k3 Raph was in the SAINW episode... Hopefully it's going okay :S**

 **SlenderGrl, I'm so glad you're enjoying the story! And thank you very much! ^w^**


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